1NFT - JenaLib

Title :   OVOTRANSFERRIN, N-TERMINAL LOBE, IRON LOADED OPEN FORM

Authors :   K. Mizutani, H. Yamashita, H. Kurokawa, B. Mikami, M. Hirose

Date :   07 Jan 99 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (6x)

Keywords :   Transferrin, Ovotransferrin, Iron Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Mizutani, H. Yamashita, H. Kurokawa, B. Mikami, M. Hirose
Alternative Structural State Of Transferrin. The Crystallographic Analysis Of Iron-Loaded But Domain-Opened Ovotransferrin N-Lobe.
J. Biol. Chem. V. 274 10190 1999
PubMed-ID: 10187803 | Reference-DOI: 10.1074/JBC.274.15.10190

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_001 *	A	83	V	TRFE_CHICK	---	---	A	V	64	V
2	UniProt	VAR_TRFE_CHICK_002 *	V	100	I	TRFE_CHICK	---	---	A	V	81	I
3	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	A	R	135	W
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_001 *	A	83	V	TRFE_CHICK	---	---	A	V	64	V
2	UniProt	VAR_TRFE_CHICK_002 *	V	100	I	TRFE_CHICK	---	---	A	V	81	I
3	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	A	R	135	W
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_001 *	A	83	V	TRFE_CHICK	---	---	A	V	64	V
2	UniProt	VAR_TRFE_CHICK_002 *	V	100	I	TRFE_CHICK	---	---	A	V	81	I
3	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	A	R	135	W
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (4, 4)

Asymmetric Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_CHICK	26-352 364-689	1	A:7-332 -
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_CHICK	111-120 450-459	1	A:92-101 -
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_CHICK	210-226 543-558	1	A:191-207 -
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_CHICK	242-272 584-614	1	A:223-253 -

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_CHICK	26-352 364-689	1	A:7-332 -
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_CHICK	111-120 450-459	1	A:92-101 -
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_CHICK	210-226 543-558	1	A:191-207 -
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_CHICK	242-272 584-614	1	A:223-253 -

Biological Unit 2 (4, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_CHICK	26-352 364-689	6	A:7-332 -
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_CHICK	111-120 450-459	6	A:92-101 -
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_CHICK	210-226 543-558	6	A:191-207 -
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_CHICK	242-272 584-614	6	A:223-253 -

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:329
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:329
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
           TRFE_CHICK    23 KSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR 351
               SCOP domains d1nfta_ A: Ovotransferrin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1nftA01 A:5-81,A:251-316 Periplasmic binding protein-like II                 1nftA02 A:82-250,A:317-327 Periplasmic binding protein-like II                                                                                                           1nftA01 A:5-81,A:251-316 Periplasmic binding protein-like II      1nftA02    ----- CATH domains
               Pfam domains ---Transferrin-1nftA01 A:7-332                                                                                                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh......eee.hhhhhhhh......eeeeeeee.......eeeeeeeeee......hhh....eeee.........hhhhhhhhh.............hhhhhhh...eeee......hhhh..................hhhhhhhhhh.....eeeee..hhhhh.hhhhhheeee.....eeehhhhhh...eeee..eeee.....hhhhhhhhhhhhhhh..................hhh........eeeeee......hhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------V----------------I-----------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TRANSFERRIN_LIKE_4  PDB: A:7-332 UniProt: 26-352                                                                                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nft A   4 KSVIRWCTVSSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLIHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR 332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (TRFE_CHICK | P02789)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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